%!PS-Adobe-3.0 EPSF-3.0
%%Title: Sequence Logo : 
%%Creator: 
%%CreationDate: 
%%BoundingBox:   0  0  226  141 
%%Pages: 0
%%DocumentFonts: 
%%EndComments

% * globin.fasta: aligned globin sequences
% * Lamprey GLOBIN V - SEA LAMPREY
% * Hagfish GLOBIN III - ATLANTIC HAGFISH
% * Frog HEMOGLOBIN BETA CHAIN - EDIBLE FROG
% * African Elephant HEMOGLOBIN BETA CHAIN - AFRICAN ELEPHANT
% * Goat HEMOGLOBIN BETA-A CHAIN - GOAT
% * Primate HEMOGLOBIN BETA CHAIN - HUMAN, CHIMPANZEES, AND GORILLA
% * Gibbon HEMOGLOBIN BETA CHAIN - COMMON GIBBON (TENTATIVE SEQUENCE)
% * Dog HEMOGLOBIN BETA CHAIN - DOG AND COYOTE
% * Horse HEMOGLOBIN BETA CHAIN - HORSE
% * Human, Chimp HEMOGLOBIN GAMMA CHAINS - HUMAN AND CHIMPANZEE
% * Nile Crocodile HEMOGLOBIN BETA CHAIN - NILE CROCODILE
% * Chicken HEMOGLOBIN BETA CHAIN - CHICKEN
% * NA Opossum HEMOGLOBIN BETA CHAIN - NORTH AMERICAN OPOSSUM
% * Carp HEMOGLOBIN BETA CHAINS - CARP
% * Shark HEMOGLOBIN BETA CHAIN - PORT JACKSON SHARK
% * Shark HEMOGLOBIN ALPHA CHAIN - PORT JACKSON SHARK
% * Carp HEMOGLOBIN ALPHA CHAIN - CARP
% * Bullfrog HEMOGLOBIN ALPHA CHAIN - BULLFROG TADPOLE
% * Nile Crocodile HEMOGLOBIN ALPHA CHAIN - NILE CROCODILE
% * Ostrich HEMOGLOBIN ALPHA CHAIN - OSTRICH
% * Kangaroo HEMOGLOBIN ALPHA CHAIN - EASTERN GRAY KANGAROO
% * Armadillo HEMOGLOBIN ALPHA CHAIN - NINE-BANDED ARMADILLO
% * Horse HEMOGLOBIN ALPHA CHAINS - HORSE
% * Primate HEMOGLOBIN ALPHA CHAIN - HUMAN AND CHIMPANZEES
% * Macaque HEMOGLOBIN ALPHA CHAIN - RHESUS MACAQUE AND JAPANESE MACAQUE
% * Badger HEMOGLOBIN ALPHA CHAIN - EURASIAN BADGER
% * Ind Elephant HEMOGLOBIN ALPHA CHAIN - INDIAN ELEPHANT
% * Hyrax HEMOGLOBIN ALPHA CHAIN - ABYSSINIAN HYRAX
% * Tuna MYOGLOBIN - YELLOWFIN TUNA
% * Shark MYOGLOBIN - PORT JACKSON SHARK
% * Turtle MYOGLOBIN - MAP TURTLE
% * Chicken MYOGLOBIN - CHICKEN
% * Dog MYOGLOBIN - DOG, BAT-EARED FOX, AFRICAN HUNTING DOG, AND CAPE FOX
% * Badger MYOGLOBIN - EURASIAN BADGER
% * Dolphin MYOGLOBIN - SADDLEBACK DOLPHIN
% * Horse, Zebra MYOGLOBIN - HORSE AND PLAINS ZEBRA
% * African Elephant MYOGLOBIN - AFRICAN ELEPHANT
% * Aardvark MYOGLOBIN - AARDVARK
% * Human MYOGLOBIN - HUMAN
% * Macaque MYOGLOBIN - CRAB-EATING MACAQUE (TENTATIVE SEQUENCE)
% * NA Opossum MYOGLOBIN - NORTH AMERICAN OPOSSUM
% * Earthworm GLOBIN AIII - COMMON EARTHWORM
% * T heterochaetus GLOBIN, EXTRACELLULAR,
% * SMALL CHAIN - TYLORRHYNCHUS HETEROCHAETUS
% * BloodwormGLOBIN, MAJOR MONOMERIC COMPONENT - BLOODWORM
% * Whelk GLOBIN - WHELK
% * Snail GLOBIN - WATER SNAIL
% * Clam GLOBIN I - BLOOD CLAM
% * Midge larvaGLOBIN CTT-II BETA - MIDGE LARVA
% * Midge larva GLOBINS CTT-I AND CTT-IA - MIDGE LARVA
% * Bacteria BACTERIAL HEMOGLOBIN - VITREOSCILLA SP
% * P andersonii ONLEGUME HEMOGLOBIN I - PARASPONIA ANDERSONII
% * Yellow Lupin LEGHEMOGLOBIN I - YELLOW LUPIN
% * Garden Pea LEGHEMOGLOBIN I - GARDEN PEA
% * Broad Bean LEGHEMOGLOBIN I - BROAD BEAN
% * Soybean LEGHEMOGLOBIN C1 - SOYBEAN
% * Kidney Bean LEGHEMOGLOBIN A - KIDNEY BEAN
% * PROTEIN ALIGNMENT


% ---- CONSTANTS ----
/cmfactor 72 2.54 div def % defines points -> cm conversion
/cm {cmfactor mul} bind def % defines centimeters


% ---- VARIABLES ----

/black [0 0 0] def
/red [0.8 0 0] def
/green [0 0.8 0] def
/blue [0 0 0.8] def
/yellow [1 0.7 1.0] def
/purple [0.8 0 0.8] def
/orange [1 0.7 0] def


/logoWidth 8 cm def
/logoHeight 5 cm def
/logoTitle () def

/yaxis false def
/yaxisLabel (bits) def
/yaxisBits  4.3 def % bits
/yaxisTicBits 1 def


/xaxis false def
/xaxisLabel () def
/showEnds (-) def % d: DNA, p: PROTEIN, -: none

/showFineprint true def
/fineprint () def

/charsPerLine 231 def
/logoLines 1 def

/showingBox (n) def    %n s f
/shrinking false def
/shrink  1 def
/outline false def

/IbeamFraction  1 def
/IbeamGray      0.50 def
/IbeamLineWidth 0.5 def

/fontsize       12 def
/titleFontsize  14 def
/smallFontsize   6 def

/defaultColor black def 

/colorDict <<

>> def

% Standard DNA/RNA color scheme
% /colorDict << 
%   (G)  orange
%   (T)  red   
%   (C)  blue  
%   (A)  green 
%   (U)  red   
% >> def

% Standard Amino Acid colors
%/colorDict << 
%  (G)  green  
%  (S)  green  
%  (T)  green  
%  (Y)  green  
%  (C)  green  
%  (N)  purple 
%  (Q)  purple 
%  (K)  blue   
%  (R)  blue   
%  (H)  blue   
%  (D)  red    
%  (E)  red    
%  (P)  black  
%  (A)  black  
%  (W)  black  
%  (F)  black  
%  (L)  black  
%  (I)  black  
%  (M)  black  
%  (V)  black  
%>> def



% ---- DERIVED PARAMETERS ----

/leftMargin
  fontsize 3.5 mul

def 

/bottomMargin
  fontsize 0.75 mul

  % Add extra room for axis
  xaxis {fontsize 1.75 mul add } if
  xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def


/topMargin 
  logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def

/rightMargin 
  %Add extra room if showing ends
  showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def

/yaxisHeight 
  logoHeight 
  bottomMargin sub  
  topMargin sub
def

/ticWidth fontsize 2 div def

/pointsPerBit yaxisHeight yaxisBits div  def

/isBoxed 
  showingBox (s) eq
  showingBox (f) eq or { 
    true
  } {
    false
  } ifelse
def

/stackMargin 1 def

% Do not add space aroung characters if characters are boxed
/charRightMargin 
  isBoxed { 0.0 } {stackMargin} ifelse
def

/charTopMargin 
  isBoxed { 0.0 } {stackMargin} ifelse
def

/charWidth
  logoWidth
  leftMargin sub
  rightMargin sub
  charsPerLine div
  charRightMargin sub
def

/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def

/stackWidth 
  charWidth charRightMargin add
def
 
/numberFontsize 
  fontsize charWidth lt {fontsize}{charWidth} ifelse
def

% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX  fontsize neg         def
/leftEndDeltaY  fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul     def
/rightEndDeltaY leftEndDeltaY        def

% Outline width is proporional to charWidth, 
% but no less that 1 point
/outlinewidth 
  charWidth 32 div dup 1 gt  {}{pop 1} ifelse
def


% ---- PROCEDURES ----

/StartLogo { 
  % Save state
  save 
  gsave 

  % Print Logo Title, top center 
  gsave 
    SetTitleFont

    logoWidth 2 div
    logoTitle
    stringwidth pop 2 div sub
    logoHeight logoLines mul  
    titleFontsize sub
    moveto

    logoTitle
    show
  grestore

  % Print X-axis label, bottom center
  gsave
    SetStringFont

    logoWidth 2 div
    xaxisLabel stringwidth pop 2 div sub
    fontsize 3 div
    moveto

    xaxisLabel
    show
  grestore

  % Show Fine Print
  showFineprint {
    gsave
      SetSmallFont
      logoWidth
        fineprint stringwidth pop sub
        smallFontsize sub
          smallFontsize 3 div
      moveto
    
      fineprint show
    grestore
  } if

  % Move to lower left corner of last line, first stack
  leftMargin bottomMargin translate

  % Move above first line ready for StartLine 
  0 logoLines logoHeight mul translate

  SetLogoFont
} bind def

/EndLogo { 
  grestore 
  showpage 
  restore 
} bind def


/StartLine{ 
  % move down to the bottom of the line:
  0 logoHeight neg translate
  
  gsave 
    yaxis { MakeYaxis } if
    xaxis { ShowLeftEnd } if
} bind def

/EndLine{ 
    xaxis { ShowRightEnd } if
  grestore 
} bind def


/MakeYaxis {
  gsave    
    stackMargin neg 0 translate
    ShowYaxisBar
    ShowYaxisLabel
  grestore
} bind def


/ShowYaxisBar { 
  gsave  
    SetStringFont

    /str 10 string def % string to hold number  
    /smallgap stackMargin 2 div def

    % Draw first tic and bar
    gsave    
      ticWidth neg 0 moveto 
      ticWidth 0 rlineto 
      0 yaxisHeight rlineto
      stroke
    grestore

   
    % Draw the tics
    % initial increment limit proc for
    0 yaxisTicBits yaxisBits abs %cvi
    {/loopnumber exch def

      % convert the number coming from the loop to a string
      % and find its width
      loopnumber 10 str cvrs
      /stringnumber exch def % string representing the number

      stringnumber stringwidth pop
      /numberwidth exch def % width of number to show

      /halfnumberheight
         stringnumber CharBoxHeight 2 div
      def

      numberwidth % move back width of number
      neg loopnumber pointsPerBit mul % shift on y axis
      halfnumberheight sub % down half the digit

      moveto % move back the width of the string

      ticWidth neg smallgap sub % Move back a bit more  
      0 rmoveto % move back the width of the tic  

      stringnumber show
      smallgap 0 rmoveto % Make a small gap  

      % now show the tic mark
      0 halfnumberheight rmoveto % shift up again
      ticWidth 0 rlineto
      stroke
    } for
  grestore
} bind def

/ShowYaxisLabel {
  gsave
    SetStringFont

    % How far we move left depends on the size of
    % the tic labels.
    /str 10 string def % string to hold number  
    yaxisBits yaxisTicBits div cvi yaxisTicBits mul 
    str cvs stringwidth pop
    ticWidth 1.5 mul  add neg  


    yaxisHeight
    yaxisLabel stringwidth pop
    sub 2 div

    translate
    90 rotate
    0 0 moveto
    yaxisLabel show
  grestore
} bind def


/StartStack {  % <stackNumber> startstack
  xaxis {MakeNumber}{pop} ifelse
  gsave
} bind def

/EndStack {
  grestore
  stackWidth 0 translate
} bind def


% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
  gsave
    /char exch def
    /bits exch def

    /bitsHeight 
       bits pointsPerBit mul 
    def

    /charHeight 
       bitsHeight charTopMargin sub
       dup 
       0.0 gt {}{pop 0.0} ifelse % if neg replace with zero 
    def 
 
    charHeight 0.0 gt {
      char SetColor
      charWidth charHeight char ShowChar

      showingBox (s) eq { % Unfilled box
        0 0 charWidth charHeight false ShowBox
      } if

      showingBox (f) eq { % Filled box
        0 0 charWidth charHeight true ShowBox
      } if

    } if

  grestore

  0 bitsHeight translate 
} bind def


/ShowChar { % <width> <height> <char> ShowChar
  gsave
    /tc exch def    % The character
    /ysize exch def % the y size of the character
    /xsize exch def % the x size of the character

    /xmulfactor 1 def 
    /ymulfactor 1 def

  
    % if ysize is negative, make everything upside down!
    ysize 0 lt {
      % put ysize normal in this orientation
      /ysize ysize abs def
      xsize ysize translate
      180 rotate
    } if

    shrinking {
      xsize 1 shrink sub 2 div mul
        ysize 1 shrink sub 2 div mul translate 

      shrink shrink scale
    } if

    % Calculate the font scaling factors
    % Loop twice to catch small correction due to first scaling
    2 {
      gsave
        xmulfactor ymulfactor scale
      
        ysize % desired size of character in points
        tc CharBoxHeight 
        dup 0.0 ne {
          div % factor by which to scale up the character
          /ymulfactor exch def
        } % end if
        {pop pop}
        ifelse

        xsize % desired size of character in points
        tc CharBoxWidth  
        dup 0.0 ne {
          div % factor by which to scale up the character
          /xmulfactor exch def
        } % end if
        {pop pop}
        ifelse
      grestore
    } repeat

    % Adjust horizontal position if the symbol is an I
    tc (I) eq {
      charWidth 2 div % half of requested character width
      tc CharBoxWidth 2 div % half of the actual character
      sub 0 translate
      % Avoid x scaling for I 
      /xmulfactor 1 def 
    } if


    % ---- Finally, draw the character
  
    newpath
    xmulfactor ymulfactor scale

    % Move lower left corner of character to start point
    tc CharBox pop pop % llx lly : Lower left corner
    exch neg exch neg
    moveto

    outline {  % outline characters:
      outlinewidth setlinewidth
      tc true charpath
      gsave 1 setgray fill grestore
      clip stroke
    } { % regular characters
      tc show
    } ifelse

  grestore
} bind def


/ShowBox { % x1 y1 x2 y2 filled ShowBox
  gsave
    /filled exch def 
    /y2 exch def
    /x2 exch def
    /y1 exch def
    /x1 exch def
    newpath
    x1 y1 moveto
    x2 y1 lineto
    x2 y2 lineto
    x1 y2 lineto
    closepath

    clip
    
    filled {
      fill
    }{ 
      0 setgray stroke   
    } ifelse

  grestore
} bind def


/MakeNumber { % number MakeNumber
  gsave
    SetNumberFont
    stackWidth 0 translate
    90 rotate % rotate so the number fits
    dup stringwidth pop % find the length of the number
    neg % prepare for move
    stackMargin sub % Move back a bit
    charWidth (0) CharBoxHeight % height of numbers
    sub 2 div %
    moveto % move back to provide space
    show
  grestore
} bind def


/Ibeam{ % heightInBits Ibeam
  gsave
    % Make an Ibeam of twice the given height in bits
    /height exch  pointsPerBit mul def 
    /heightDRAW height IbeamFraction mul def

    IbeamLineWidth setlinewidth
    IbeamGray setgray 

    charWidth2 height neg translate
    ShowIbar
    newpath
      0 0 moveto
      0 heightDRAW rlineto
    stroke
    newpath
      0 height moveto
      0 height rmoveto
      currentpoint translate
    ShowIbar
    newpath
    0 0 moveto
    0 heightDRAW neg rlineto
    currentpoint translate
    stroke
  grestore
} bind def


/ShowIbar { % make a horizontal bar
  gsave
    newpath
      charWidth4 neg 0 moveto
      charWidth4 0 lineto
    stroke
  grestore
} bind def


/ShowLeftEnd {
  gsave
    SetStringFont
    leftEndDeltaX leftEndDeltaY moveto
    showEnds (d) eq {(5) show ShowPrime} if
    showEnds (p) eq {(N) show} if
  grestore
} bind def


/ShowRightEnd { 
  gsave
    SetStringFont
    rightEndDeltaX rightEndDeltaY moveto
    showEnds (d) eq {(3) show ShowPrime} if
    showEnds (p) eq {(C) show} if
  grestore
} bind def


/ShowPrime {
  gsave
    SetPrimeFont
    (\242) show 
  grestore
} bind def

 
/SetColor{ % <char> SetColor
  dup colorDict exch known {
    colorDict exch get aload pop setrgbcolor
  } {
    pop
    defaultColor aload pop setrgbcolor
  } ifelse 
} bind def

% define fonts
/SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
/SetLogoFont  {/Helvetica-Narrow-Bold findfont charWidth  scalefont setfont} bind def
/SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
/SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def

/SetNumberFont {
    /Helvetica-Bold findfont 
    numberFontsize
    scalefont
    setfont
} bind def

%Take a single character and return the bounding box
/CharBox { % <char> CharBox <lx> <ly> <ux> <uy>
  gsave
    newpath
    0 0 moveto
    % take the character off the stack and use it here:
    true charpath 
    flattenpath 
    pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
    % the path is here, but toss it away ...
  grestore
} bind def


% The height of a characters bounding box
/CharBoxHeight { % <char> CharBoxHeight <num>
  CharBox
  exch pop sub neg exch pop
} bind def


% The width of a characters bounding box
/CharBoxWidth { % <char> CharBoxHeight <num>
  CharBox
  pop exch pop sub neg 
} bind def


% Deprecated names
/startstack {StartStack} bind  def
/endstack {EndStack}     bind def
/makenumber {MakeNumber} bind def
/numchar { MakeSymbol }  bind def

%%EndProlog

%%Page: 1 1
StartLogo
StartLine % line number 1

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endstack

(2) startstack
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endstack

(3) startstack
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endstack

(4) startstack
 4.32192809488736 (D) numchar
endstack

(5) startstack
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endstack

(6) startstack
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(7) startstack
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(8) startstack
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(9) startstack
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(10) startstack
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(15) startstack
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(16) startstack
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(17) startstack
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(18) startstack
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(19) startstack
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(20) startstack
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(21) startstack
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(22) startstack
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(23) startstack
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(24) startstack
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(25) startstack
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(26) startstack
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(27) startstack
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(28) startstack
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(29) startstack
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endstack

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endstack

(35) startstack
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endstack

(36) startstack
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endstack

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EndLine
EndLogo

%%EOF



















